Business and Biopdiversity - Ch 4 - Snowball Pilot

Setup

Code
#|
if (!exists("params")) {
    params <- rmarkdown::yaml_front_matter("~/Documents_Local/git/IPBES_data_tsu/Assessments/Business/IPBES_BBA_Ch4-Snowball_Pilot_1/snowball.qmd")$params
}

# library(bibtex)
library(openalexR)
Thank you for using openalexR!
To acknowledge our work, please cite the package by calling
`citation("openalexR")`.
Code
library(writexl)
library(tibble)
library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
Code
library(ggplot2)
library(ggraph)
library(tidygraph)

Attaching package: 'tidygraph'
The following object is masked from 'package:stats':

    filter
Code
library(knitr)

list.files(
    "R",
    full.names = TRUE,
    recursive = TRUE
) |>
    sapply(
        FUN <- source
    )
        R/plot_snowball.R R/to_xlsx.R
value   ?                 ?          
visible FALSE             FALSE      
Code
kp <- read.csv(file.path("Key Papers", params$key_paper))

Back to Readme

Searches

OpenAlex

Setup OpelAnex usage and do snowball serarch

Code
#|

fn <- file.path("data", "key_works.rds")
if (file.exists(fn)) {
    key_works <- readRDS(fn)
} else {
    key_works <- oa_fetch(
        entity = "works",
        doi = kp$DOI,
        verbose = FALSE
    )
    saveRDS(key_works, fn)
}


ids <- openalexR:::shorten_oaid(key_works$id)

fn <- file.path(".", "data", "snowball.rds")
if (file.exists(fn)) {
    snowball <- readRDS(fn)
} else {
    snowball <- oa_snowball(
        identifier = ids,
        verbose = FALSE
    )
    saveRDS(snowball, fn)
}

flat_snow <- snowball2df(snowball) |>
    as_tibble()

Save snowball as Excel file (snowball_excel.xlsx)

Code
#|

###

fn <- file.path(".", "data", "snowball.xlsx")
if (!file.exists(fn)) {
    to_xlsx(
        snowball = snowball,
        flat_snow = flat_snow,
        xls_filename = fn
    )
}

The column are: (the Concept columns are not that relevant at the moment)

  • id: internal id fromOpenAlex
  • author: authors of the paper
  • publication_year: publication year
  • title: title of the paper
  • doi: doi of the paper
  • no_referenced_works: number of references in the paper which are also in OpenAlex
  • cited_global: Number of times the paper has been cited
  • cited_global_per_year: standardised number of times cirted (cited_global / number of years published)
  • no_connections: number of connections in the rgaph, i.e. either cited or citing a paper in the snowball corpus
  • concepts_l0: Concept 0. level assigned by OpenAlex
  • concepts_l1: Concept 1. level assigned by OpenAlex
  • concepts_l2: Concept 2. level assigned by OpenAlex
  • concepts_l3: Concept 3. level assigned by OpenAlex
  • concepts_l4: Concept 4. level assigned by OpenAlex
  • concepts_l5: Concept 5. level assigned by OpenAlex
  • author_institute: Institute of the authors
  • institute_country: Country of the institute
  • abstract: the abstract of the paper

Identification of references with more than one edge

This is the number of connections (connection_count)of the paper (id)

Code
#|
mult_edge <- flat_snow |>
    select(id, connection_count) |>
    filter(connection_count > 1) |>
    arrange(desc(connection_count))

links <- flat_snow |>
    filter(id %in% mult_edge$id)

links |>
    select(id, display_name, publication_year, doi, connection_count) |>
    arrange(desc(connection_count)) |>
    knitr::kable()
id display_name publication_year doi connection_count
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